Any Cytognosis computational result published after 2026 should be verifiable and
re-runnable by a third party using only public resources and a single command:
``bash`
cytoskeleton reproduce
| # | Principle | Key technology |
|---|---|---|
| P1 | cytoskeleton is the single asset and environment manager | VFS, RO-Crate emitter, schema registry |
| P2 | LinkML is the single schema source of truth | Compiles to Pydantic, JSON Schema, GraphQL, OWL, ShEx, SHACL, SQL DDL, TypeScript |
| P3 | Artifacts are content-addressed; configs reference them by ID | SWHID (code), DVC md5 (data), sha256 (blobs), OCI digest (images) |
| P4 | Environments and containers are signed and pinned | uv lockfiles, OCI images, sigstore, pixi |
| P5 | Every run emits a Workflow Run Crate (WRROC) | RO-Crate + in-toto attestation + OTel trace |
| P6 | FAIRDOM-SEEK + WorkflowHub are the public hubs | Self-hosted SEEK, workflowhub.eu |
mermaid
flowchart TB
classDef schema fill:#E8F1F8,stroke:#4A7BAF
classDef repro fill:#FFF8DC,stroke:#998A4F
classDef hub fill:#F1F8E8,stroke:#7BAF4A
classDef store fill:#F5F5F5,stroke:#666
subgraph SCHEMA["Schema Layer"]
LML["LinkML schema\n(source of truth)"]:::schema
PYDT["Pydantic types"]:::schema
JSONS["JSON Schema"]:::schema
OWL["OWL / ShEx / SHACL"]:::schema
TS["TypeScript types"]:::schema
LML --> PYDT & JSONS & OWL & TS
end
subgraph EXEC["Execution Layer"]
VFS["cytoskeleton VFS\n(content-addressed URIs)"]:::repro
RUNNER["cytoskeleton run\n(redun · Nextflow · Snakemake · DVC)"]:::repro
INTOTO["in-toto attestation\n(DSSE envelope)"]:::repro
CRATE["WRROC emitter\n(RO-Crate 1.1)"]:::repro
VFS --> RUNNER --> INTOTO --> CRATE
end
subgraph STORE["Content Stores"]
SWH["Software Heritage\n(code, SWHID)"]:::store
DVC["DVC remote\n(data, md5)"]:::store
OCI["GCP Artifact Registry\n(images, digest)"]:::store
ZEN["Zenodo / DOI\n(published crates)"]:::store
end
subgraph HUBS["Discovery Hubs"]
SEEK["hub.cytognosis.org\n(FAIRDOM-SEEK)"]:::hub
WH["workflows.cytognosis.org\n(WorkflowHub)"]:::hub
LM["LifeMonitor\n(CI health badges)"]:::hub
FAIRHub["FAIRDOMHub / workflowhub.eu\n(public mirrors)"]:::hub
end
SCHEMA --> EXEC
EXEC --> STORE
CRATE --> HUBS
WH --> LM
`
Document Map
| Doc | Contents |
|---|---|
| schema-strategy.md | LinkML as single schema source; compilation targets; ISA, RO-Crate, GA4GH alignment |
| artifact-vfs-swhid.md | Virtual File System design; content-addressing; driver implementations; hash strategy |
| envs-containers.md | 66-cell env matrix; OCI image policy; sigstore signing; SLSA L3 |
| provenance-lineage.md | in-toto attestation; DSSE envelopes; WRROC/Process Run Crate/Five Safes Crate structure |
| seek-workflowhub.md | SEEK/WorkflowHub deployment; LifeMonitor; FAIRSCAPE; public mirroring |
| acceptance-kpis.md | Definitions of "Reproducible", "FAIR Workflow", "FAIR Dataset", "FAIR Model"; monthly KPIs |
Implementation Phases
| Phase | What | Status |
|---|---|---|
| cytoskeleton v2 core | VFS drivers, WRROC emitter, schema registry | ⏳ In design |
| First cytos migration | Migrate biolink source config to VFS + SWHID | ⏳ Pending cytoskeleton v2 |
| SEEK bring-up | Deploy FAIRDOM-SEEK on Cloud Run | ⏳ Phase 11 (infrastructure) |
| WorkflowHub bring-up | Deploy WorkflowHub on Cloud Run | ⏳ Phase 11 |
| cytos full migration | All 10 source configs + dvc.yaml generated from LinkML | ⏳ Phase 6 |
| Yar integration | Capture pipeline emits Process Run Crates | ⏳ Phase 7 |
| Public mirroring | workflowhub.eu + FAIRDOMHub Programme registration | ⏳ With first public release |
Quick-Start Verification Commands
`bash
Validate a published Crate
cytoskeleton verify crate
Reproduce a published run
cytoskeleton reproduce
Verify a code SWHID against a local checkout
cytoskeleton verify swhid /path/to/repo
Verify a container image signature + CVEs
cytoskeleton verify image us-central1-docker.pkg.dev/.../cytognosis-base:v2.1.0
Full audit of a local run
cytoskeleton audit run .crates//
`
Success Criterion
At EOY 2026, a researcher outside Cytognosis can:
1. Find a Cytognosis result on Zenodo / Google Scholar.
2. Run
cytoskeleton reproduce .
3. Have the workflow re-execute, pulling code by SWHID, image by OCI digest, and data by sha256.
4. Receive outputs whose hashes match within numerical tolerance (REPRODUCIBLE or EQUIVALENT).
5. See LifeMonitor green badge confirming the workflow's tests still pass.
6. Generate a BibTeX entry via cytoskeleton cite`.